Blues came third in their group on 10 points - just one point behind Club Brugge and Braga who shared a 1-1 draw in Belgium.
Hughton said: "We did what we could do by winning and it is disappointing not to go through when you have ended up with 10 points.
"Normally you would find that would be enough to qualify. But it has been a terrific learning curve for us and the lads deserve real credit.
"The two sides that have gone through have got vastly more experience of Europe than ourselves."
A goal from Adam Rooney, created by man of the match Nathan Redmond, earned victory for Blues.
Redmond, 17, tormented the Maribor defence before leaving the pitch to a standing ovation when substituted two minutes from time.
But Hughton is keen to keep his progress as a player in perspective.
He said: "He is a young lad still developing. There will be ups and downs for him.
"He will come up against sturdy full-backs and not always get his own way.
"But the Europa League will have benefited him with his development."